i believe this is the key to unlock your transforms: trans_mni2anat=" -i anat2mni_Affine.txt anat2mni_InverseWarp.nii.gz " trans_anat2func="-i raiders_func2anat_Affine.txt" trans_mni2func=" $trans_anat2func $trans_mni2anat "
switch both aff/inv and the trans order .... On Fri, Jul 16, 2010 at 5:28 PM, Yaroslav Halchenko <[email protected]> wrote: > Package: ants > Version: 1.9+svn532-3 > Severity: normal > > P.S. CCing all possibly interested parties ;) > > According to docstring of WarpTimeSeriesImageMultiTransform sequence of > necessary transformations could be arbitrarily long. Having applied a > sequence > > MNI -> inverse warp -> inverse affine -> inverse affine > > produces different (and looks like incorrect) result from if I do > transformations in two steps, e.g. > > MNI -> inverse warp -> inverse affine > > and then result of previous given for the final inverse affine. > > Here is output of running reproduce.sh. All data, script and > results are available from > > http://www.onerussian.com/Linux/bugs/ants.2steps/ > > I investigate the result by comparing mni2bold.nii.gz and mni2bold-2.nii.gz > overlayed on top of epi_template.nii.gz. mni2bold.nii.gz seems to be offset > toward anterior > > $> ./reproduce.sh > I: Lets do directly all the steps at once > Running: WarpTimeSeriesImageMultiTransform 4 mni.nii.gz mni2bold.nii.gz -R > epi_template.nii.gz anat2mni_InverseWarp.nii.gz -i anat2mni_Affine.txt -i > raiders_func2anat_Affine.txt --use-NN > FIELD: anat2mni_InverseWarp.nii.gz > AFFINE-INV: anat2mni_Affine.txt > AFFINE-INV: raiders_func2anat_Affine.txt > moving_image_filename: mni.nii.gz > output_image_filename: mni2bold.nii.gz > reference_image_filename: epi_template.nii.gz > [0/3]: FIELD: anat2mni_InverseWarp.nii.gz > [1/3]: AFFINE-INV: anat2mni_Affine.txt > [2/3]: AFFINE-INV: raiders_func2anat_Affine.txt > Four-D image size: [182, 218, 182, 1] > 4D-In-Spc [1, 1, 1, 1] > 4D-In-Org [-90, 126, -72, 0] > 4D-In-Size [182, 218, 182, 1] > 4D-In-Dir 1 0 0 0 > 0 -1 0 0 > 0 0 1 0 > 0 0 0 1 > > ...... > 4D-Out-Spc [3, 3, 3, 1] > 4D-Out-Org [-70.5, -75.759, 93.1085, 0] > 4D-Out-Size [64, 64, 48, 1] > 4D-Out-Dir -0 0 1 0 > 1 -0 0 0 > 0 -1 -0 0 > 0 0 0 1 > > Use Nearest Neighbor interpolation > 0 % done ... -0 0 1 > 1 -0 0 > 0 -1 -0 > > 100 % complete > I: Lets do directly all the steps at once > Step 1 mni->anat: WarpTimeSeriesImageMultiTransform 4 mni.nii.gz > mni2anat.nii.gz -R brain_avg.nii.gz anat2mni_InverseWarp.nii.gz -i > anat2mni_Affine.txt --use-NN > FIELD: anat2mni_InverseWarp.nii.gz > AFFINE-INV: anat2mni_Affine.txt > moving_image_filename: mni.nii.gz > output_image_filename: mni2anat.nii.gz > reference_image_filename: brain_avg.nii.gz > [0/2]: FIELD: anat2mni_InverseWarp.nii.gz > [1/2]: AFFINE-INV: anat2mni_Affine.txt > Four-D image size: [182, 218, 182, 1] > 4D-In-Spc [1, 1, 1, 1] > 4D-In-Org [-90, 126, -72, 0] > 4D-In-Size [182, 218, 182, 1] > 4D-In-Dir 1 0 0 0 > 0 -1 0 0 > 0 0 1 0 > 0 0 0 1 > > ...... > 4D-Out-Spc [1, 1, 1, 1] > 4D-Out-Org [-86.8253, -128, 132.723, 0] > 4D-Out-Size [256, 256, 176, 1] > 4D-Out-Dir -0 0 1 0 > 1 -0 0 0 > 0 -1 -0 0 > 0 0 0 1 > > Use Nearest Neighbor interpolation > 0 % done ... -0 0 1 > 1 -0 0 > 0 -1 -0 > > 100 % complete > Step 2 anat->mni: WarpTimeSeriesImageMultiTransform 4 mni2anat.nii.gz > mni2bold-2.nii.gz -R epi_template.nii.gz -i raiders_func2anat_Affine.txt > --use-NN > AFFINE-INV: raiders_func2anat_Affine.txt > moving_image_filename: mni2anat.nii.gz > output_image_filename: mni2bold-2.nii.gz > reference_image_filename: epi_template.nii.gz > [0/1]: AFFINE-INV: raiders_func2anat_Affine.txt > Four-D image size: [256, 256, 176, 1] > 4D-In-Spc [1, 1, 1, 1] > 4D-In-Org [-86.8253, -128, 132.723, 0] > 4D-In-Size [256, 256, 176, 1] > 4D-In-Dir -0 0 1 0 > 1 -0 0 0 > 0 -1 -0 0 > 0 0 0 1 > > ...... > 4D-Out-Spc [3, 3, 3, 1] > 4D-Out-Org [-70.5, -75.759, 93.1085, 0] > 4D-Out-Size [64, 64, 48, 1] > 4D-Out-Dir -0 0 1 0 > 1 -0 0 0 > 0 -1 -0 0 > 0 0 0 1 > > > > > -- System Information: > Debian Release: squeeze/sid > APT prefers unstable > APT policy: (901, 'unstable'), (900, 'testing'), (300, 'experimental') > Architecture: amd64 (x86_64) > > Kernel: Linux 2.6.32-5-amd64 (SMP w/2 CPU cores) > Locale: LANG=en_US, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) > Shell: /bin/sh linked to /bin/bash > > Versions of packages ants depends on: > ii libc6 2.11.2-2 Embedded GNU C Library: Shared > lib > ii libgcc1 1:4.4.4-6 GCC support library > ii libinsighttoolkit3.18 3.18.0-3+b1 Image processing toolkit for > regis > ii libstdc++6 4.4.4-6 The GNU Standard C++ Library v3 > > ants recommends no packages. > > Versions of packages ants suggests: > ii fsl 4.1.6-1 analysis tools for FMRI, MRI and > D > pn gridengine-client <none> (no description available) > > -- no debconf information > > -- > .-. > =------------------------------ /v\ ----------------------------= > Keep in touch // \\ (yoh@|www.)onerussian.com > Yaroslav Halchenko /( )\ ICQ#: 60653192 > Linux User ^^-^^ [175555] > > > > > -- ß®∫∆π -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected]
